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More than 7,000 Kyrgyz residents have been evacuated from the area engulfed by the fighting as troops from the two countries exchanged gunfire around a water supply facility near the village of Kok-Tash in western Kyrgyzstan on the border with Tajikistan.
Despite a cease-fire declared late Thursday, Kyrgyz officials reported some firing Friday.
Kyrgyzstan’s Health Ministry said 13 people died and 134 others were injured in the clashes.
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A large part of the Tajik-Kyrgyz border has remained unmarked, fueling fierce disputes over water, land and pastures.
Kyrgyz and Tajik delegations have held several rounds of talks in recent years but have failed to end the border controversy.
Both nations have claimed the area around the water supply facility in Kok-Tash, a dispute dating back decades to when they were both part of the Soviet Union.
The latest conflict erupted Wednesday when Tajik officials attempted to mount surveillance cameras to monitor the water supply facility amid the tensions over water distribution, and the Kyrgyz residents opposed the move.
The Kyrgyz and the Tajiks began hurling stones at each other and troops quickly entered the fray.
Kyrgyzstan and Tajikistan are both members of the Russia-dominated Collective Security Treaty Organization.
The Russian Foreign Ministry on Friday voiced concern about the conflict and urged them to negotiate a lasting settlement.